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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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DV.7.1+S:K478R, Orf1a_V1143F=nsp3_V325F 9 seqs in England, Spain and Netherland as of 10-10 #737

Closed krosa1910 closed 1 year ago

krosa1910 commented 1 year ago

Descendent of DV.7.1 (judged from flip+S:L858I +CH*) Mutations on top of that: C10228T ( small, 6 seq branch)+ T20833C, A29172T (N:H300L) C10615T, A22995G (S:K478R) Inquiry of this lineage:Spike_L455F,L858I,T478R
Nucleotides query: T4036A,C10228T,22995G,C19017T (edited again) Sequence 1/First is EPI_ISL_18107088 from Luxemburg in 23-07-10 Sequence 2/Second is EPI_ISL_18209326 from England in 23-08-12 Downsampled tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2d0a4_3efad0.json?f_userOrOld=uploaded%20sample DV.7.1 tree: (edited) Schermata 2023-09-03 alle 08 57 20 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_e8a5_42dff0.json?c=gt-S_478&label=id:node_7689922 Schermata 2023-09-03 alle 08 57 44

It is rather rare that CH* got S:T478R mutation, and it is interesting when the second sequence is in a foreign country (although it's probably also because Luxemberg is so small)

FedeGueli commented 1 year ago

Thank you @krosa1910 very good spot, i've edited slighty the proposal adding a more specific tree and a nuc query.

krosa1910 commented 1 year ago

Grow to 4 seemingly, spread to Spain.

krosa1910 commented 1 year ago
Screenshot 2023-09-07 at 5 43 53 AM

The latest 3 seem to form a branch with the mutation orf1a:V1143F=nsp3_V325F, and it is predicted to be positive and showed up in a weird long past mutant B.1.1.433, which created a temporary spread in Denmark back in 2020 winter.

FedeGueli commented 1 year ago

thank you please propose it when it reaches 10

krosa1910 commented 1 year ago

Spain and Scotland have some new updates. Also, the earliest Luxemburg sequence is excluded.

FedeGueli commented 1 year ago

Better keeping it track here for a while. It didnt take off while it could and now it is likely too late.

krosa1910 commented 1 year ago

Better keeping it track here for a while. It didnt take off while it could and now it is likely too late.

Agree, now it seem nowhere to compete with stronger variants like HK.3 or BA.2.86.1, I don't even mention JN.1. I guess DV.7.1 lost its window to gain more privilege position in Europe as a whole, and could only remain their as a "normal FLip". with low frequency, just like CH.1 in 2022 winter.

FedeGueli commented 1 year ago

It did not be successful